diff --git a/bin/wt-metadata-export b/bin/wt-metadata-export
index ee6e5fd..42545dd 100755
--- a/bin/wt-metadata-export
+++ b/bin/wt-metadata-export
@@ -154,7 +154,7 @@ if [[ "$SKIP_CONFIRM" != "true" ]]; then
   echo
 fi
 
-# Find all metadata directories and deduplicate
+# Find all metadata directories and prune nested paths
 # Outputs: one path per line, with nested paths removed
 # (e.g., if .ijwb contains .idea, only .ijwb is listed)
 find_all_metadata_dirs() {
@@ -166,34 +166,11 @@ find_all_metadata_dirs() {
     done < <(find "$SOURCE_DIR" -maxdepth 5 -type d -name "$pattern" 2>/dev/null)
   done
 
-  # No metadata found
   if [[ ${#all_paths[@]} -eq 0 ]]; then
     return
   fi
 
-  # Sort paths (shorter paths come first)
-  local sorted_paths
-  sorted_paths=$(printf '%s\n' "${all_paths[@]}" | sort)
-
-  # Deduplicate: skip paths that are inside another metadata path
-  local kept_paths=()
-  while IFS= read -r _entry_path; do
-    [[ -z "$_entry_path" ]] && continue
-    local dominated=false
-
-    for kept in ${kept_paths[@]+"${kept_paths[@]}"}; do
-      # Check if $_p is inside $kept (kept is a prefix of _p)
-      if [[ "$_entry_path" == "$kept/"* ]]; then
-        dominated=true
-        break
-      fi
-    done
-
-    if [[ "$dominated" == "false" ]]; then
-      kept_paths+=("$_entry_path")
-      echo "$_entry_path"
-    fi
-  done <<< "$sorted_paths"
+  printf '%s\n' "${all_paths[@]}" | _wt_prune_nested_paths
 }
 
 echo "Finding and deduplicating metadata directories..."
diff --git a/bin/wt-metadata-import b/bin/wt-metadata-import
index 76f8e4e..85adffb 100755
--- a/bin/wt-metadata-import
+++ b/bin/wt-metadata-import
@@ -186,63 +186,69 @@ copy_real_metadata() {
   cp -a "$real_path" "$dst"
 }
 
-# Import a single pattern
-# Args: $1 = pattern name (e.g., ".ijwb")
-import_pattern() {
-  local pattern="$1"
-  local count=0
-
-  echo "Importing '$pattern' directories..."
-
-  # Find all matching directories (symlinks or real directories) under the source directory
-  # Use -L to follow symlinks (source path might be a symlink)
-  # Note: Use process substitution (< <(...)) instead of pipe to avoid subshell variable scope issues
-  while IFS= read -r -d '' META_SRC; do
-    # Parent dir relative to SOURCE_DIR
-    PARENT_SRC="$(dirname "$META_SRC")"
-
-    # Handle pattern at root (PARENT_SRC == SOURCE_DIR)
-    if [[ "$PARENT_SRC" == "$SOURCE_DIR" ]]; then
-      REL_PATH=""
-    else
-      REL_PATH="${PARENT_SRC#"$SOURCE_DIR"/}"
-    fi
+# Find all metadata directories across all patterns and prune nested paths.
+# Uses -L to follow symlinks in the vault.
+# Outputs: one path per line, with nested paths removed.
+find_all_import_dirs() {
+  local all_paths=()
+
+  for pattern in $WT_METADATA_PATTERNS; do
+    while IFS= read -r _entry_path; do
+      [[ -n "$_entry_path" ]] && all_paths+=("$_entry_path")
+    done < <(find -L "$SOURCE_DIR" \( -type l -o -type d \) -name "$pattern" -print 2>/dev/null)
+  done
+
+  if [[ ${#all_paths[@]} -eq 0 ]]; then
+    return
+  fi
 
-    # Corresponding target parent
-    if [[ -z "$REL_PATH" ]]; then
-      TARGET_PARENT="$TARGET_DIR"
-    else
-      TARGET_PARENT="$TARGET_DIR/$REL_PATH"
-    fi
-    TARGET_META="$TARGET_PARENT/$pattern"
+  printf '%s\n' "${all_paths[@]}" | _wt_prune_nested_paths
+}
 
-    echo "  Found source: $META_SRC"
-    echo "  -> Installing to: $TARGET_META"
+# Import all metadata directories (pruned across patterns)
+count=0
+while IFS= read -r META_SRC; do
+  [[ -z "$META_SRC" ]] && continue
 
-    mkdir -p "$TARGET_PARENT"
+  pattern="$(basename "$META_SRC")"
+  PARENT_SRC="$(dirname "$META_SRC")"
 
-    if [[ -e "$TARGET_META" || -L "$TARGET_META" ]]; then
-      rm -rf "$TARGET_META"
-    fi
+  if [[ "$PARENT_SRC" == "$SOURCE_DIR" ]]; then
+    REL_PATH=""
+  else
+    REL_PATH="${PARENT_SRC#"$SOURCE_DIR"/}"
+  fi
 
-    if ! copy_real_metadata "$META_SRC" "$TARGET_META"; then
-      echo "     Skipping due to broken symlink"
-      echo "     Removing broken symlink from vault: $META_SRC"
-      rm -f "$META_SRC"
-    fi
+  if [[ -z "$REL_PATH" ]]; then
+    TARGET_PARENT="$TARGET_DIR"
+  else
+    TARGET_PARENT="$TARGET_DIR/$REL_PATH"
+  fi
+  TARGET_META="$TARGET_PARENT/$pattern"
+
+  echo "  Found source: $META_SRC"
+  echo "  -> Installing to: $TARGET_META"
 
-    count=$((count + 1))
-  done < <(find -L "$SOURCE_DIR" \( -type l -o -type d \) -name "$pattern" -print0 2>/dev/null)
+  mkdir -p "$TARGET_PARENT"
 
-  if [[ $count -eq 0 ]]; then
-    echo "  (no '$pattern' directories found in vault)"
+  if [[ -e "$TARGET_META" || -L "$TARGET_META" ]]; then
+    rm -rf "$TARGET_META"
+  fi
+
+  if ! copy_real_metadata "$META_SRC" "$TARGET_META"; then
+    echo "     Skipping due to broken symlink"
+    echo "     Removing broken symlink from vault: $META_SRC"
+    rm -f "$META_SRC"
   fi
-}
 
-# Import each configured pattern
-for pattern in $WT_METADATA_PATTERNS; do
-  import_pattern "$pattern"
+  count=$((count + 1))
+done < <(find_all_import_dirs)
+
+if [[ $count -eq 0 ]]; then
+  echo "  (no metadata directories found in vault)"
+else
   echo
-done
+  echo "Imported $count metadata directories."
+fi
 
 success "Done importing metadata."
diff --git a/lib/wt-common b/lib/wt-common
index 8cd19bc..cf4dc25 100644
--- a/lib/wt-common
+++ b/lib/wt-common
@@ -373,6 +373,31 @@ _wt_expand_path() {
   echo "${path/#\~\//$HOME/}"
 }
 
+# Prune paths where an ancestor is already in the set.
+# When metadata patterns nest (e.g., .ijwb contains .idea), only the
+# outermost directory needs to be exported/imported — the children are
+# already included.
+# Reads newline-separated absolute paths from stdin, writes pruned paths to stdout.
+_wt_prune_nested_paths() {
+  local sorted
+  sorted=$(sort)
+  local kept_paths=()
+  while IFS= read -r _entry_path; do
+    [[ -z "$_entry_path" ]] && continue
+    local dominated=false
+    for kept in ${kept_paths[@]+"${kept_paths[@]}"}; do
+      if [[ "$_entry_path" == "$kept/"* ]]; then
+        dominated=true
+        break
+      fi
+    done
+    if [[ "$dominated" == "false" ]]; then
+      kept_paths+=("$_entry_path")
+      echo "$_entry_path"
+    fi
+  done <<< "$sorted"
+}
+
 # Check if a path value is valid for a directory config variable.
 # Valid means: absolute path (starts with /) and contains no glob characters.
 # Args: $1 = path value
diff --git a/lib/wt-context-setup b/lib/wt-context-setup
index 05c893b..fc7621c 100644
--- a/lib/wt-context-setup
+++ b/lib/wt-context-setup
@@ -124,23 +124,10 @@ _wt_detect_metadata_patterns() {
     return
   fi
 
-  local sorted_paths
-  sorted_paths=$(printf '%s\n' "${all_paths[@]}" | sort)
-
   local kept_paths=()
   while IFS= read -r _entry_path; do
-    [[ -z "$_entry_path" ]] && continue
-    local dominated=false
-    for kept in ${kept_paths[@]+"${kept_paths[@]}"}; do
-      if [[ "$_entry_path" == "$kept/"* ]]; then
-        dominated=true
-        break
-      fi
-    done
-    if [[ "$dominated" == "false" ]]; then
-      kept_paths+=("$_entry_path")
-    fi
-  done <<< "$sorted_paths"
+    [[ -n "$_entry_path" ]] && kept_paths+=("$_entry_path")
+  done < <(printf '%s\n' "${all_paths[@]}" | _wt_prune_nested_paths)
 
   local patterns=()
   for _entry_path in ${kept_paths[@]+"${kept_paths[@]}"}; do
diff --git a/test/integration/wt-metadata-import.bats b/test/integration/wt-metadata-import.bats
index f40ce20..ea9d241 100644
--- a/test/integration/wt-metadata-import.bats
+++ b/test/integration/wt-metadata-import.bats
@@ -258,3 +258,33 @@ teardown() {
     assert [ -f "$WORKTREE/.idea/config.xml" ]
     assert_equal "$(cat "$WORKTREE/.idea/config.xml")" "config content"
 }
+
+# =============================================================================
+# Nested metadata pruning tests
+# =============================================================================
+
+@test "wt-metadata-import does not import nested metadata inside parent pattern" {
+    sed -i.bak 's/WT_METADATA_PATTERNS=".*"/WT_METADATA_PATTERNS=".ijwb .idea"/' "$TEST_HOME/.wt/repos/test.conf"
+
+    # Create .ijwb containing .idea in the real repo (standard Bazel plugin structure)
+    mkdir -p "$REPO/myproject/.ijwb/.idea"
+    echo "config" > "$REPO/myproject/.ijwb/config.xml"
+    echo "idea-config" > "$REPO/myproject/.ijwb/.idea/workspace.xml"
+
+    # Export to vault first (creates symlinks, which is the real-world structure)
+    run "$TEST_HOME/.wt/bin/wt-metadata-export" -y
+    assert_success
+    # Vault should have a symlink for .ijwb, not a separate .idea entry
+    assert [ -L "$WT_IDEA_FILES_BASE/myproject/.ijwb" ]
+
+    # Import into worktree
+    run "$TEST_HOME/.wt/bin/wt-metadata-import" -y "$WT_IDEA_FILES_BASE" "$WORKTREE"
+    assert_success
+
+    # .ijwb should be imported (with .idea inside it via the copy)
+    assert [ -d "$WORKTREE/myproject/.ijwb" ]
+    assert [ -f "$WORKTREE/myproject/.ijwb/.idea/workspace.xml" ]
+
+    # Output should NOT show a separate .idea import for the nested dir
+    refute_output --partial "myproject/.ijwb/.idea"
+}
diff --git a/test/unit/wt-common.bats b/test/unit/wt-common.bats
index 0f953b5..0397a44 100644
--- a/test/unit/wt-common.bats
+++ b/test/unit/wt-common.bats
@@ -754,6 +754,35 @@ teardown() {
     assert_equal "$WT_BASE_BRANCH" "pre-existing"
 }
 
+# =============================================================================
+# Tests for _wt_prune_nested_paths()
+# =============================================================================
+
+@test "_wt_prune_nested_paths removes nested paths" {
+    result=$(printf '%s\n' "/a/.ijwb" "/a/.ijwb/.idea" "/b/.idea" | _wt_prune_nested_paths)
+    assert_equal "$result" "$(printf '%s\n' "/a/.ijwb" "/b/.idea")"
+}
+
+@test "_wt_prune_nested_paths keeps siblings" {
+    result=$(printf '%s\n' "/a/.idea" "/a/.ijwb" | _wt_prune_nested_paths)
+    assert_equal "$result" "$(printf '%s\n' "/a/.idea" "/a/.ijwb")"
+}
+
+@test "_wt_prune_nested_paths handles empty input" {
+    result=$(printf '' | _wt_prune_nested_paths)
+    assert_equal "$result" ""
+}
+
+@test "_wt_prune_nested_paths handles single path" {
+    result=$(printf '%s\n' "/a/.idea" | _wt_prune_nested_paths)
+    assert_equal "$result" "/a/.idea"
+}
+
+@test "_wt_prune_nested_paths handles multi-level nesting" {
+    result=$(printf '%s\n' "/a/.ijwb" "/a/.ijwb/.idea" "/a/.ijwb/.idea/.run" | _wt_prune_nested_paths)
+    assert_equal "$result" "/a/.ijwb"
+}
+
 # =============================================================================
 # Tests for _wt_is_valid_path_config()
 # =============================================================================